Re: protein folding cg

From: Joshua Adelman (
Date: Fri Jun 05 2009 - 02:01:51 CDT

There are definitely RBCG-like force-fields out there that fold at get
reasonable tertiary structure. I am by no means an expert, but for
instance there is a CA based force-field from the Head-Gordon group
that seems to work for a small model protein:
Yap, EH et al (2008) A coarse-grained alpha-carbon protein model with
anisotropic hydrogen-bonding. Proteins 70(3) :626-38
This FF has an term that attempts to capture the h-bonding found in
secondary structure. It isn't implemented in NAMD, but it (and the
references therein) might give you some ideas of what's out there.

As far as the time it takes to fold a given protein, this will depend
entirely on the protein, its size, the choice of force-field and
certainly a whole host of other factors related to the simulation
(solvent model, temperature, etc).

Best of luck and trying doing a search of the literature to see what
has been attempted and what has been reasonably successful as a
starting point. And certainly, I defer to people who have much more
experience trying to simulate folding events using CG models.


On Jun 4, 2009, at 11:21 PM, doty alexiou wrote:

> Hello.I would like to have an opinion of somebody who had experience
> with protein folding using the RBCG approach and NAMD.I read that
> the protein will not obtain the tertiary structure because of the
> lack of hydrogen bonds.But do we expect the protein to create the
> apropriate secondary structure as seen in the native?And if so,how
> many nanoseconds should the simulation run in order to see it?thank u!

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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